3

IQ study involving hormone
thyroid disease has repercussions on the medical and molecular biology fields

Rresults of a related studyo with thyroid hormone, obtained by master's student Leandro Martínez, from the Institute of Chemistry (IQ) at Unicamp, are causing good repercussions among researchers in Brazil and the United States. Martínez carried out computational simulations of already recognized importance as guides for experimental work, in the dissertation "Computational study of the mechanisms of dissociation of thyroid hormone from its nuclear receptor", supervised by professors Munir Skaf, from IQ, and Igor Polikarpov, from USP in São Carlos .

Nuclear receptors form a family of approximately 40 proteins, which have the function of regulating the transcription of genes within the cell nucleus - hence, their name. Despite the uncertain data, the intensity of research into this family can be measured by the fact that between 15% and 30% of the medicines produced in the world, mainly contraceptives, act in one way or another on nuclear receptors. Thyroid hormone and its nuclear receptor, specifically, control metabolic rates and cardiac activity, being associated with obesity or hyperactivity disorders.

"Proteins are not absorbed by the body in the way we ingest them. Once digested, the body will synthesize in the cells the proteins that we actually use, from amino acids", Professor Munir Skaf seeks to simplify. "Our body needs different proteins for its different activities. Which of the proteins is being synthesized at each moment depends on the body's regulatory mechanisms", adds Leandro Martínez.

Nuclear receptors, therefore, regulate whether or not the proteins encoded by genes are being produced in the organism. They interact directly with DNA, through specific connections with well-defined nucleotide sequences (fundamental parts of DNA) for each gene. Receptors activate or inhibit the transcription of these genes, and this is the first step in the protein synthesis process in cells. However, activation or inhibition depends on the receptors binding to small molecules, hormones. Hormones are known for approximately half of the identified nuclear receptors. Among the most cited are thyroid hormone, progesterone, estrogen and vitamin A (retinoic acid).

The receptor may be present in the body, but not necessarily linked to the hormone; alone, it is inactive. "The hormone enters and leaves the protein. It is very important to understand these association and dissociation mechanisms, not only for scientific knowledge, but also for the rational development of drugs that act on these proteins in a way analogous to hormones", says Martínez. In the case of thyroid hormone, this would mean ensuring control of the body's fat content, helping to solve obesity and heart problems.

Simulations - The structures of several nuclear receptors, linked or not to hormones, have recently been known through complex processes such as X-ray diffraction. However, the mechanisms of association and dissociation are not known. There are only two studies in the literature, referring to the dissociation of hormones from their receptors and both dealing with retinoic acid. This research was carried out by two different American groups (Martin Karplus at Harvard and Klaus Schulten at Urbana), using different computer simulation techniques using the molecular dynamics method. In this third study, aimed at the dissociation of thyroid hormone from its nuclear receptor, Leandro Martínez used the combination of the two previous techniques.

"The structures are very complex and obtaining them depends on exhaustive work. Such structures, whether or not they have a hormone inside, are static and provide little information about the dynamics of the protein. Information about the entry and exit of the hormone is generally obtained by speculation on the static structure or indirect experiments. Simulations allow the direct visualization of these molecular processes in great detail. This is where our work comes in", informs Martínez.

Results- Simulations at the Unicamp Chemistry Institute indicated three mechanisms for the release of thyroid hormone from its receptor. With the same patience and availability required for the long series of computer simulations, the advisor and advisor sought to describe didactically the step-by-step search for possible paths, as well as the equally relevant interactions observable along the way. So many details, however, could confuse the layman, taking away the focus on the importance of the results.

The first relevant result is that the mechanism obtained in previous simulations on retinoic acid was repeated in simulations of the dissociation of thyroid hormone. Due to a lack of other evidence, this mechanism was generally accepted by the scientific community for the entire class of nuclear receptors. It was demonstrated for the first time, directly, that this mechanism may also exist for other families of receptors. However, this mechanism, called "mousetrap", had already been questioned in the literature because in it the hormone must enter through a region of the receptor that is generally blocked by the presence of another protein, known as a coactivator.

The most promising results concern two other mechanisms obtained by Leandro Martínez - one of them unpublished in the international literature - which present consistent correlations with several experimental results, in addition to being free of the problems inherent to the "mousetrap" mechanism because they involve other regions of the receptor. . In what was called mechanism 2, the hormone enters in a way that explains the binding of several synthetic ligands that have been developed at the University of California, according to the article published on this page. The third mechanism, in turn, has already been suggested in the literature, but simulations showed that it must be the main dissociation mechanism in vivo as it presents lower energetic barriers. The simulations reopened, with new arguments, the debate about these mechanisms, and seem to have revealed more consistent ways in which receptors can recognize hormones in the body.

Endocrinologists and biophysicists evaluate results with interest The results achieved by Leandro Martínez, on mechanisms of association and dissociation of thyroid hormone with its nuclear receptor, will have a great impact if they are confirmed through experimental work. This confirmation has been sought by the group led by professor Igor Polikarpov, from USP in São Carlos, and by a group of endocrinologists led by professor John Baxter, from the University of California. The two teams have been working in cooperation in the area of ​​nuclear receptors since 2001. Martínez got involved with the topic as a scientific initiation student of Polikarpov at the National Synchrotron Light Laboratory and was joined by a group of physical chemists led by professor Munir Skaf, from the Institute of Chemistry from Unicamp, completing the support tripod for his master's thesis. Part of the complex computational programs were implemented with the help of another IQ student, Milton Sonoda. American endocrinologists were very impressed with mechanism #2, as several drug prototypes they are developing are consistent with thyroid hormone entering the protein through this pathway. "Our simulations showed regions of the protein that are mobile. Using this information, they can arrive at ligands larger than the natural hormone, that is, molecules that will also interact effectively with the protein, although different", explains Martínez. Another important aspect for future research, in the opinion of Professor Munir Skaf, is the possibility of carrying out site-directed mutations, using synthetic techniques to promote amino acid exchanges until reaching those most effective for stabilizing the hormone within the protein. "With the mechanisms we suggest, researchers have a better idea of ​​the regions where mutations can be promoted. They can start from another level," he says. According to Leandro Martínez, the simulations indicated around ten key amino acids, among the 256 that the protein has: "Scientists will have a much clearer basis. These groups have been working with proteins for 20 years, but this area is very open to information. As these structural chemistry problems are quite complicated, every type of new information, arising from simulations or experiments, results in a very big leap. The expectation is that our work will be useful for these groups. And the feedback has been very positive" .

Top